Variant report

Variant	rs9429076
Chromosome Location	chr1:45819489-45819490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45480214..45482710-chr1:45817452..45819904,2	K562	blood:
2	chr1:45819408..45822200-chr1:45957439..45959167,2	K562	blood:

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1006216	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs1007858	0.82[EUR][1000 genomes]
rs1084166	0.83[EUR][1000 genomes]
rs10890327	0.86[EUR][1000 genomes]
rs10890330	0.90[CEU][hapmap]
rs11211101	1.00[CEU][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11211108	0.87[EUR][1000 genomes]
rs11211111	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs11211117	0.83[EUR][1000 genomes]
rs11211118	0.83[EUR][1000 genomes]
rs11211124	0.81[CEU][hapmap]
rs12029322	0.81[CEU][hapmap]
rs12037201	0.84[EUR][1000 genomes]
rs12037411	0.93[EUR][1000 genomes]
rs12046816	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs12097497	0.86[EUR][1000 genomes]
rs12139364	0.83[JPT][hapmap]
rs12410493	0.85[EUR][1000 genomes]
rs1417578	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1494812	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1538969	0.83[EUR][1000 genomes]
rs1538970	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17395553	0.92[EUR][1000 genomes]
rs1771551	0.82[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1826691	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2050884	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2055145	0.90[CEU][hapmap]
rs2088100	0.86[EUR][1000 genomes]
rs2153607	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2153608	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2153609	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2185549	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2298018	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2487442	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2492836	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2492840	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28555082	0.83[EUR][1000 genomes]
rs3219463	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3219472	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3219476	0.80[AFR][1000 genomes]
rs3219489	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3790582	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs4520450	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap]
rs4633317	0.81[CEU][hapmap]
rs4660301	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4660849	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4660851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4660852	1.00[CEU][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4660853	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4660854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660855	0.85[EUR][1000 genomes]
rs4660858	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs4660863	0.81[CEU][hapmap]
rs61788261	0.85[EUR][1000 genomes]
rs61788262	0.81[EUR][1000 genomes]
rs61788281	0.83[EUR][1000 genomes]
rs61791362	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61791368	0.84[EUR][1000 genomes]
rs61791369	0.87[EUR][1000 genomes]
rs6657284	0.95[CEU][hapmap]
rs713358	0.81[CEU][hapmap]
rs72686460	0.83[EUR][1000 genomes]
rs7417107	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525849	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7528573	0.83[EUR][1000 genomes]
rs7531253	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs7532762	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7536135	0.86[EUR][1000 genomes]
rs7543428	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7544178	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7553318	1.00[CEU][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs781226	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs781230	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs781232	0.82[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs868351	0.81[CEU][hapmap]
rs884962	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9326141	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9429072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9429073	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9429074	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9429158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9429159	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9429160	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9429161	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9429076	MMACHC	cis	multi-tissue	Pritchard
rs9429076	MUTYH	cis	multi-tissue	Pritchard

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45806600-45821600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:45807200-45825800	Weak transcription	Small Intestine	intestine
3	chr1:45808800-45825600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:45810000-45819800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:45810600-45825600	Weak transcription	Fetal Kidney	kidney
6	chr1:45810800-45820800	Weak transcription	HUVEC	blood vessel
7	chr1:45811200-45820800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:45811200-45825600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:45811200-45825600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:45811200-45825600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:45811400-45825800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:45811400-45825800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:45811600-45825800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:45812000-45826000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:45812200-45825800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:45812400-45820600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:45812400-45821200	Weak transcription	Primary T cells from cord blood	blood
18	chr1:45812400-45825600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:45812400-45825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:45812600-45819600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:45812600-45825600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:45812600-45825800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:45812600-45825800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:45812600-45826400	Weak transcription	Colonic Mucosa	Colon
25	chr1:45812800-45821800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:45812800-45822200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr1:45812800-45824400	Weak transcription	Gastric	stomach
28	chr1:45812800-45825600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:45812800-45825800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:45812800-45835800	Weak transcription	Thymus	Thymus
31	chr1:45813000-45822200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:45813000-45825800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:45813200-45825800	Weak transcription	Spleen	Spleen
34	chr1:45813800-45825400	Weak transcription	Fetal Stomach	stomach
35	chr1:45815000-45820800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:45815000-45821200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:45815000-45821400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:45815200-45819800	Weak transcription	Lung	lung
39	chr1:45815200-45825600	Weak transcription	Fetal Lung	lung
40	chr1:45815200-45825800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:45815200-45825800	Weak transcription	Right Atrium	heart
42	chr1:45815400-45825600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:45815400-45825600	Weak transcription	GM12878-XiMat	blood
44	chr1:45815400-45825800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:45815400-45826000	Weak transcription	Esophagus	oesophagus
46	chr1:45815400-45826000	Weak transcription	Left Ventricle	heart
47	chr1:45815600-45825600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:45815800-45821200	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:45816000-45821400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:45816200-45821000	Weak transcription	Hela-S3	cervix

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